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- PDB-6yut: Structure of recombinant human beta-glucocerebrosidase in complex... -

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Basic information

Entry
Database: PDB / ID: 6yut
TitleStructure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30 / Cyclophellitol aziridine Inhibitor / Complex
Function / homology
Function and homology information


steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation ...steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation / lymphocyte migration / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / glucosylceramidase activity / sphingosine biosynthetic process / autophagosome organization / microglial cell proliferation / glucosyltransferase activity / regulation of TOR signaling / response to thyroid hormone / Glycosphingolipid catabolism / microglia differentiation / ceramide biosynthetic process / positive regulation of type 2 mitophagy / lipid storage / lipid glycosylation / brain morphogenesis / positive regulation of protein-containing complex disassembly / response to pH / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / pyramidal neuron differentiation / negative regulation of protein metabolic process / motor behavior / lysosome organization / Transferases; Glycosyltransferases; Hexosyltransferases / neuromuscular process / hematopoietic stem cell proliferation / antigen processing and presentation / Association of TriC/CCT with target proteins during biosynthesis / response to testosterone / response to dexamethasone / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of MAPK cascade / negative regulation of protein-containing complex assembly / cell maturation / mitophagy / cholesterol metabolic process / lysosomal lumen / cellular response to starvation / respiratory electron transport chain / determination of adult lifespan / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / T cell differentiation in thymus / neuron apoptotic process / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / signaling receptor binding / lysosomal membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-K35 / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsRowland, R.J. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: Chemistry / Year: 2021
Title: Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents.
Authors: Rowland, R.J. / Chen, Y. / Breen, I. / Wu, L. / Offen, W.A. / Beenakker, T.J. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Aerts, J.M.F.G. / Artola, M. / Overkleeft, H.S. / Davies, G.J.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z
Revision 1.2Dec 8, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glucosylceramidase
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,39946
Polymers111,2802
Non-polymers5,11944
Water13,241735
1
AAA: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,19623
Polymers55,6401
Non-polymers2,55522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,20423
Polymers55,6401
Non-polymers2,56322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.699, 285.525, 91.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-947-

HOH

21AAA-958-

HOH

31BBB-904-

HOH

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Glucosylceramidase / Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / D-glucosyl-N- ...Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / D-glucosyl-N-acylsphingosine glucohydrolase / Imiglucerase


Mass: 55640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant human beta-glucocerebrosidase lacking its 40-amino acid signalling sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, EC: 3.2.1.104

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Sugars , 2 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 773 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-K35 / ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]pentanamide


Mass: 277.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H23NO6 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.03 M KCl, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.76→47.633 Å / Num. obs: 143462 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Net I/σ(I): 10
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7028 / CC1/2: 0.835 / Rpim(I) all: 0.37 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NT0

2nt0


Resolution: 1.76→47.633 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.919 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2084 7160 4.992 %
Rwork0.183 --
all0.184 --
obs-143436 99.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.049 Å2
Baniso -1Baniso -2Baniso -3
1-5.597 Å20 Å20 Å2
2---2.895 Å20 Å2
3----2.702 Å2
Refinement stepCycle: LAST / Resolution: 1.76→47.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 314 735 8857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177552
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6711512
X-RAY DIFFRACTIONr_angle_other_deg1.2671.59217556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20251050
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg4.82208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05122.184403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815.0941279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.041541
X-RAY DIFFRACTIONr_chiral_restr0.0710.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021791
X-RAY DIFFRACTIONr_nbd_refined0.2020.21628
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.26903
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23900
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2563
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.218
X-RAY DIFFRACTIONr_nbd_other0.1850.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.225
X-RAY DIFFRACTIONr_mcbond_it1.9313.0484016
X-RAY DIFFRACTIONr_mcbond_other1.9313.0484015
X-RAY DIFFRACTIONr_mcangle_it2.9134.5655034
X-RAY DIFFRACTIONr_mcangle_other2.9134.5665035
X-RAY DIFFRACTIONr_scbond_it2.6493.5284424
X-RAY DIFFRACTIONr_scbond_other2.6483.5294425
X-RAY DIFFRACTIONr_scangle_it4.1925.1516478
X-RAY DIFFRACTIONr_scangle_other4.1925.1516479
X-RAY DIFFRACTIONr_lrange_it6.01637.0919360
X-RAY DIFFRACTIONr_lrange_other6.01637.0919361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8060.3625550.3599968X-RAY DIFFRACTION99.8008
1.806-1.8550.3425000.3229775X-RAY DIFFRACTION99.9514
1.855-1.9090.2844870.2989482X-RAY DIFFRACTION100
1.909-1.9680.2675320.2739193X-RAY DIFFRACTION99.9178
1.968-2.0320.2484650.248956X-RAY DIFFRACTION99.9152
2.032-2.1030.2054250.2168708X-RAY DIFFRACTION99.8906
2.103-2.1830.2324240.1978357X-RAY DIFFRACTION99.7388
2.183-2.2720.2314270.1958015X-RAY DIFFRACTION99.7754
2.272-2.3730.2394280.1947736X-RAY DIFFRACTION99.9633
2.373-2.4890.2254000.1847390X-RAY DIFFRACTION99.8846
2.489-2.6230.2173460.1777056X-RAY DIFFRACTION99.8516
2.623-2.7820.2133670.1686646X-RAY DIFFRACTION99.3484
2.782-2.9740.2233120.1716264X-RAY DIFFRACTION99.5007
2.974-3.2130.2062790.1685869X-RAY DIFFRACTION99.8376
3.213-3.5190.1893030.1695397X-RAY DIFFRACTION99.6329
3.519-3.9340.162420.1454872X-RAY DIFFRACTION98.8786
3.934-4.5420.1482270.1264313X-RAY DIFFRACTION99.105
4.542-5.5620.1692160.1343696X-RAY DIFFRACTION99.542
5.562-7.8590.1971460.1672898X-RAY DIFFRACTION99.3473
7.859-47.6330.181790.1771686X-RAY DIFFRACTION98.8242

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